there are a couple of mods I want to open up with notepad so that I can change somethings.but I'm afraid the game then won't recognize the file and then I won't be able to use that mod again.is it safe to open files with notepad?.

Why use noetepad, when you can use Construction Set that comes with the game?

The only thing you can modify with Notepad would be the ini file. Which already is in Notepad.
Use the CS.